A new model for parent-of-origin effect analyses applied to Brown Swiss cattle slaughterhouse data
Genomic imprinting is a phenomenon that arises when the expression of genes depends on the parental origin of alleles. Epigenetic mechanisms may induce the full or partial suppression of maternal or paternal alleles, thereby leading to different types of imprinting. However, imprinting effects have...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2017-01-01
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| Series: | Animal |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S1751731116002391 |
| _version_ | 1818667701677064192 |
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| author | I. Blunk M. Mayer H. Hamann N. Reinsch |
| author_facet | I. Blunk M. Mayer H. Hamann N. Reinsch |
| author_sort | I. Blunk |
| collection | DOAJ |
| description | Genomic imprinting is a phenomenon that arises when the expression of genes depends on the parental origin of alleles. Epigenetic mechanisms may induce the full or partial suppression of maternal or paternal alleles, thereby leading to different types of imprinting. However, imprinting effects have received little consideration in animal breeding programmes, although their relevance to some agricultural important traits has been demonstrated. A recently proposed model (imprinting model) with two path-of-transmission (male and female)-specific breeding values for each animal accounts for all types of imprinting simultaneously (paternal, maternal, full and partial). Imprinting effects (or more generally: parent-of-origin effects (POE)) are determined by taking the difference between the two genetic effects in each animal. However, the computation of their prediction error variance (PEV) is laborious; thus, we propose a new model that is equivalent to the aforementioned imprinting model, which facilitates the direct estimation of imprinting effects instead of taking the differences and the PEV is readily obtained. We applied the new model to slaughterhouse data for Brown Swiss cattle, among which imprinting has never been investigated previously. Data were available for up to 173 051 fattening bulls, where the pedigrees contained up to 428 710 animals representing the entire Brown Swiss population of Austria and Germany. The traits analysed comprised the net BW gain, fat score, EUROP class and killing out percentage. The analysis demonstrated that the net BW gain, fat score and EUROP class were influenced significantly by POE. After estimating the POE, the new model yielded estimates with reliabilities ranging between 0.4 and 0.9. On average, the imprinting variances accounted for 9.6% of the total genetic variance, where the maternal gamete was the main contributor. Moreover, our results agreed well with those obtained using linear models when the EUROP class and fat score were treated as categorical traits by applying a GLMM with a logit link function. |
| first_indexed | 2024-12-17T06:24:37Z |
| format | Article |
| id | doaj.art-f7b7ad0e343e4cd799490801d76d7b84 |
| institution | Directory Open Access Journal |
| issn | 1751-7311 |
| language | English |
| last_indexed | 2024-12-17T06:24:37Z |
| publishDate | 2017-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Animal |
| spelling | doaj.art-f7b7ad0e343e4cd799490801d76d7b842022-12-21T22:00:20ZengElsevierAnimal1751-73112017-01-0111710961106A new model for parent-of-origin effect analyses applied to Brown Swiss cattle slaughterhouse dataI. Blunk0M. Mayer1H. Hamann2N. Reinsch3Leibniz-Institut für Nutztierbiologie (FBN), Institut für Genetik und Biometrie, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, GermanyLeibniz-Institut für Nutztierbiologie (FBN), Institut für Genetik und Biometrie, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, GermanyLandesamt für Geoinformation und Landentwicklung Baden-Württemberg, Dienststelle Kornwestheim, Stuttgarter Straße 161, 70806 Kornwestheim, GermanyLeibniz-Institut für Nutztierbiologie (FBN), Institut für Genetik und Biometrie, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, GermanyGenomic imprinting is a phenomenon that arises when the expression of genes depends on the parental origin of alleles. Epigenetic mechanisms may induce the full or partial suppression of maternal or paternal alleles, thereby leading to different types of imprinting. However, imprinting effects have received little consideration in animal breeding programmes, although their relevance to some agricultural important traits has been demonstrated. A recently proposed model (imprinting model) with two path-of-transmission (male and female)-specific breeding values for each animal accounts for all types of imprinting simultaneously (paternal, maternal, full and partial). Imprinting effects (or more generally: parent-of-origin effects (POE)) are determined by taking the difference between the two genetic effects in each animal. However, the computation of their prediction error variance (PEV) is laborious; thus, we propose a new model that is equivalent to the aforementioned imprinting model, which facilitates the direct estimation of imprinting effects instead of taking the differences and the PEV is readily obtained. We applied the new model to slaughterhouse data for Brown Swiss cattle, among which imprinting has never been investigated previously. Data were available for up to 173 051 fattening bulls, where the pedigrees contained up to 428 710 animals representing the entire Brown Swiss population of Austria and Germany. The traits analysed comprised the net BW gain, fat score, EUROP class and killing out percentage. The analysis demonstrated that the net BW gain, fat score and EUROP class were influenced significantly by POE. After estimating the POE, the new model yielded estimates with reliabilities ranging between 0.4 and 0.9. On average, the imprinting variances accounted for 9.6% of the total genetic variance, where the maternal gamete was the main contributor. Moreover, our results agreed well with those obtained using linear models when the EUROP class and fat score were treated as categorical traits by applying a GLMM with a logit link function.http://www.sciencedirect.com/science/article/pii/S1751731116002391beef traitBrown Swiss cattleepigeneticsimprinting varianceparent-of-origin effects |
| spellingShingle | I. Blunk M. Mayer H. Hamann N. Reinsch A new model for parent-of-origin effect analyses applied to Brown Swiss cattle slaughterhouse data Animal beef trait Brown Swiss cattle epigenetics imprinting variance parent-of-origin effects |
| title | A new model for parent-of-origin effect analyses applied to Brown Swiss cattle slaughterhouse data |
| title_full | A new model for parent-of-origin effect analyses applied to Brown Swiss cattle slaughterhouse data |
| title_fullStr | A new model for parent-of-origin effect analyses applied to Brown Swiss cattle slaughterhouse data |
| title_full_unstemmed | A new model for parent-of-origin effect analyses applied to Brown Swiss cattle slaughterhouse data |
| title_short | A new model for parent-of-origin effect analyses applied to Brown Swiss cattle slaughterhouse data |
| title_sort | new model for parent of origin effect analyses applied to brown swiss cattle slaughterhouse data |
| topic | beef trait Brown Swiss cattle epigenetics imprinting variance parent-of-origin effects |
| url | http://www.sciencedirect.com/science/article/pii/S1751731116002391 |
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